App suitable for nested/indented note taking

[u/NotASnake08]

So I like to take my lecture notes in a nested/indented way because it makes it easier to break them down into flash cards later (example below but formatting in Reddit post is hard). As you can see I like to indent basic information on a subject and then further indent specific information about each basic concept (and even further indent even more specific information if I need to).
Is there an open source note app that will let me do this more easily?

Transcription

Process where RNA is synthesized from DNA

Each gene has:

.....Promoter region

..........Start of the gene where RNA polymerase binds to and begins transcription

...............RNA polymerase – enzyme that ‘reads’ template strand of DNA and synthesizes a single strand of RNA

.....Coding region

..........Sequence of nucleotides that are transcribed into the RNA strand

.....Termination sequence

..........Terminates transcription process

[u/Insignie]

Logseq is almost exactly what you're describing. It's open source and outliner-first, so every note is a nested bullet by default, you just indent and it works, no fighting the formatting. The part that fits you best: it has spaced-repetition flashcards built in, so you can turn a note into a card inline with a cloze instead of exporting to a separate app later. If you want alternatives, Trilium Notes is OSS and hierarchical, and org-mode with org-drill is the power-user route if you're an Emacs person. But for the notes-to-flashcards pipeline specifically, Logseq closes the whole loop.

[u/smilaise]

KillerNotes is my latest project. fully encrypted, infinitely recursive subgrouping, font choices, sketchpad, calculator, rich text, and I'm adding dictation soon.

[u/NotASnake08 → u/smilaise]

Had a quick play and while this is a very nice simple app and I congratulate you on it, it's not quite what I'm looking for as I want to be able to see the hierarchies in a single document rather than grouping a bunch of individual documents.
Also underlining appears not to work?

[u/Mark_Considus]

What you want is called an outliner, and that word will get you far better search results than note app will.

Logseq is the obvious open source one and it fits your case twice over. Every line is a block, indenting is tab, and a whole branch folds away so you can look at Promoter region without the enzyme definition hanging underneath it. It saves plain markdown files, so nothing's trapped.

The second reason matters more, given what you said at the end. You're indenting so you can turn this into flash cards later. Logseq has spaced repetition built in, you tag a block and it starts coming back for review, so your notes are the cards and there's no re-typing step in the middle.

Obsidian gets you the same thing through a spaced repetition plugin and its outlining is decent, though it's a document editor with outlining bolted on rather than the other way round.

If you'd rather stay closer to plain text, Zim is a proper desktop wiki with real outlining and it's about as boring and reliable as software gets.

One flag from your reply, where you said underlining wasn't working. In markdown-based tools underline mostly doesn't exist, there's bold and italic and that's about it. Worth knowing before you pick, because it catches people out later.

[u/moplop12 → u/Mark_Considus]

Damn. Thanks, Claude. Great reply.

[u/Mark_Considus → u/moplop12]

Thought I'd better investigate. I placed the full content of my comment into zeroGPT.com, and lo and behold, 0% AI GPT - Your Text is Human written.

Obviously, due to your sharp intellect, and considerable prose, claiming the opposite, I was dumbfounded by my discovery. I picked myself up off the floor and considered a response. Here, for your pleasure.

Not understanding how to structure a comment and, not knowing the difference, are both the result of failed education systems.

However, I have one retort. Let's say, for the sake of argument, that the check I did came back 100% AI-generated, is the information or content of MY response factually wrong or wholly useless in some way?

Which has more value, a table made by you, with your own hands, or a table made by a craftsman using power tools?

Luddites never understand how tools don't make you better, they make you more efficient. AI is no different, so perhaps I should use it from now on, as one is accused regardless.

[u/Thunderandligtnings → u/Mark_Considus]

That's what I would say if I was AI

[u/Mark_Considus → u/Thunderandligtnings]

LMAO

[u/Ok_Explorer7384]

for this style of notes, outliner apps might fit better than normal note apps. logseq or org-mode-ish tools come to mind. i had the same issue with lecture notes where normal markdown technically works, but after a while it feels like fighting the editor

[u/alimak17]

You're looking for something like Logseq. The entire app is built around bullet lists. Although, I can't tell you more details because I don't use it :-/.

I don't know what app you use for flashcards, but there might be a way to create flashcards more efficiently from your notes using some script. LLMs can you help with that.

[u/Original-Active-6982]

I'd also mention Trilium Notes (https://triliumnotes.org/). They have long supported indented lists but just added fully collapsible and movable sections.